Glass repair and fairing putty

I am in the process of re-painting my skiff and I had a few questions. The transom had been replaced before I got her and the individual did a lousy job. I spent several hours with 60 grit sanding down all of the epoxy runs on the inside and outside. My goal is to get it smooth and then primer and repaint the interior and exterior of the hull. While sanding down the runs I noticed that there were several areas where the epoxy and glass of the transom replacement didn't fill a small crack or hole in the old fiberglass and a "bubble" was created. When I attempted to clean up the shoddy worksmanship, I uncovered the "hole". My plan is to use a filler or fairing compound to fill these gaps and then sand smooth. Has anyone used any of these compounds? 3M says it is harder than glass, will not shrink, bonds to anything and is approved for below and above the waterline. What say you experts?

Also, what would you recommend as a primer and paint for the interior/deck? I am a novice, but am hugely (for lack of a better word...anal) ;D. So I will need something that is durable and easy to work with and still get good results. Does this primer/paint combo exist? Thanks.

Let's assume the "hole" is from a bolt used to hold the motor. Take a piece of tape and block the back of the hole and fill it with thickend epoxy or some other compound that is not flexible. After it hardens grind a dimple around the hole about two inches so you end up with about a 4 inch dimple. Then take some glass and cut it in a circle and another that it larger than the first but still fits inside the dimple. Epoxy on the smaller and then larger inside and out. After it cures then you sand fair and paint.

Paint: way too many choices to give with specific information on the boat and desired effects. Each one has pro's and con's.

Photos of the damaged and or poorly done glass work. What is the best method for filling in these holes and getting a good seal? Since I am not sure what was used, I will use Epoxy to get good adhesion, since you can use epoxy on top of resin, but you can't use resin on top of epoxy. Take a look at the pics and give me your thoughts on fixing this mess. Thanks.

Inside the boat, the transoom was covered in epoxy or resin runs that have now been sanded almost flat. I will go over this area with fairing putty and then sand it all smooth. Then cover with two coats of primer and 2 coats of topside paint. So far, my plan is to use an olive drab green for the hull and Carolina Tan for the interior and decking.